| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | med | PotG aka B0855, component of Putrescine porter (characterized) | 40% | 89% | 230.7 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 41% | 78% | 206.5 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 42% | 72% | 204.1 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 42% | 72% | 204.1 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 41% | 71% | 198.4 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-maltose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 42% | 72% | 194.5 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| sucrose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 42% | 72% | 194.5 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| trehalose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 42% | 72% | 194.5 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 40% | 85% | 194.5 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-mannitol catabolism | mtlK | med | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 42% | 71% | 192.6 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 40% | 71% | 188.7 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 37% | 91% | 209.9 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 34% | 99% | 201.4 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 38% | 81% | 200.3 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 35% | 100% | 198.4 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 96% | 193 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 96% | 193 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 96% | 193 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 96% | 193 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 96% | 193 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 96% | 193 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 96% | 193 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 100% | 191 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 100% | 191 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 100% | 191 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 100% | 191 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 100% | 191 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 100% | 191 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 100% | 191 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 100% | 191 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 42% | 64% | 190.7 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 92% | 190.7 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| trehalose catabolism | malK | lo | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 34% | 99% | 189.1 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 43% | 69% | 188.7 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 34% | 97% | 188 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 43% | 66% | 188 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 34% | 96% | 186.8 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 34% | 95% | 185.7 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 34% | 99% | 185.3 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 35% | 86% | 181.8 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 75% | 177.6 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 75% | 177.6 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 75% | 177.6 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 75% | 177.6 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| L-arginine catabolism | artP | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 35% | 92% | 140.2 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 35% | 92% | 140.2 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
| L-lysine catabolism | hisP | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 35% | 92% | 140.2 | Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) | 62% | 420.6 |
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know